1
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Hontani Y, Mehlhorn J, Domratcheva T, Beck S, Kloz M, Hegemann P, Mathes T, Kennis JTM. Spectroscopic and Computational Observation of Glutamine Tautomerization in the Blue Light Sensing Using Flavin Domain Photoreaction. J Am Chem Soc 2023; 145:1040-1052. [PMID: 36607126 PMCID: PMC9853863 DOI: 10.1021/jacs.2c10621] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Blue light sensing using flavin (BLUF) domains constitute a family of flavin-binding photoreceptors of bacteria and eukaryotic algae. BLUF photoactivation proceeds via a light-driven hydrogen-bond switch among flavin adenine dinucleotide (FAD) and glutamine and tyrosine side chains, whereby FAD undergoes electron and proton transfer with tyrosine and is subsequently re-oxidized by a hydrogen back-shuttle in picoseconds, constituting an important model system to understand proton-coupled electron transfer in biology. The specific structure of the hydrogen-bond patterns and the prevalence of glutamine tautomeric states in dark-adapted (DA) and light-activated (LA) states have remained controversial. Here, we present a combined femtosecond stimulated Raman spectroscopy (FSRS), computational chemistry, and site-selective isotope labeling Fourier-transform infrared spectroscopy (FTIR) study of the Slr1694 BLUF domain. FSRS showed distinct vibrational bands from the FADS1 singlet excited state. We observed small but significant shifts in the excited-state vibrational frequency patterns of the DA and LA states, indicating that these frequencies constitute a sensitive probe for the hydrogen-bond arrangement around FAD. Excited-state model calculations utilizing four different realizations of hydrogen bond patterns and glutamine tautomeric states were consistent with a BLUF reaction model that involved glutamine tautomerization to imidic acid, accompanied by a rotation of its side chain. A combined FTIR and double-isotope labeling study, with 13C labeling of FAD and 15N labeling of glutamine, identified the glutamine imidic acid C═N stretch vibration in the LA state and the Gln C═O in the DA state. Hence, our study provides support for glutamine tautomerization and side-chain rotation in the BLUF photoreaction.
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Affiliation(s)
- Yusaku Hontani
- Department
of Physics and Astronomy, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, De Boelelaan, The Netherlands
| | - Jennifer Mehlhorn
- Institut
für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Tatiana Domratcheva
- Department
of Biomolecular Mechanisms, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany,Department
of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sebastian Beck
- Department
of Chemistry, Humboldt-Universität
zu Berlin, Brook-Taylor-Str.
2, 12489 Berlin, Germany
| | - Miroslav Kloz
- Department
of Physics and Astronomy, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, De Boelelaan, The Netherlands,Institute
of Physics, ELI-Beamlines, Na Slovance 2, 182
21 Praha 8, Czech Republic
| | - Peter Hegemann
- Institut
für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Tilo Mathes
- Department
of Physics and Astronomy, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, De Boelelaan, The Netherlands,Institut
für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - John T. M. Kennis
- Department
of Physics and Astronomy, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, De Boelelaan, The Netherlands,
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2
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Shim JG, Cho SG, Kim SH, Chuon K, Meas S, Choi A, Jung KH. Heliorhodopsin Helps Photolyase to Enhance the DNA Repair Capacity. Microbiol Spectr 2022; 10:e0221522. [PMID: 36219103 PMCID: PMC9769723 DOI: 10.1128/spectrum.02215-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/24/2022] [Indexed: 01/06/2023] Open
Abstract
Light quality is a significant factor for living organisms that have photosensory systems, such as rhodopsin, a seven alpha-helical transmembrane protein with the retinal chromophore. Here, we report, for the first time, the function of new rhodopsin, which is an inverted 7-transmembrane protein, isolated from Trichococcus flocculiformis. T. flocculiformis heliorhodopsin (TfHeR) works as a regulatory helper rhodopsin that binds with class 2 cyclobutane pyrimidine dimer (CPDII) photolyase to broaden the spectrum and upregulate DNA repair activity. We have confirmed their interaction through isothermal titration calorimetry (dissociation constant of 21.7 μM) and identified the charged residues for the interaction. Based on in vivo and in vitro experiments, we showed that the binding of heliorhodopsin with photolyase improved photolyase activity by about 3-fold to repair UV-caused DNA damage. Also, the DNA repair activity of TfHeR/T. flocculiformis photolyase (TfPHR) was observed in the presence of green light. Our results suggested that heliorhodopsin directly controls the activity of photolyase and coevolves to broaden the activity spectrum by protein-protein interaction. IMPORTANCE This study reports a function for Heliorhodopsin working as a regulatory helper rhodopsin that with CPDII photolyase to broaden the spectrum and upregulating the DNA repair activity. Our results suggested that heliorhodopsin directly controls photolyase activity and coevolves to broaden the DNA repair capacity by protein-protein interaction.
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Affiliation(s)
- Jin-gon Shim
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Shin-Gyu Cho
- Department of Life Science, Sogang University, Seoul, South Korea
- Research Institute for Basic Science, Sogang University, Seoul, South Korea
| | - Se-Hwan Kim
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Kimleng Chuon
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Seanghun Meas
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Ahreum Choi
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang-gun, Gyeongsangbuk-do, South Korea
| | - Kwang-Hwan Jung
- Department of Life Science, Sogang University, Seoul, South Korea
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3
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Ghosh S, Puranik M. Initial Excited State Dynamics of Lumichrome upon Ultraviolet Excitation. Photochem Photobiol 2022; 98:1270-1283. [PMID: 35380739 DOI: 10.1111/php.13631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/01/2022] [Indexed: 11/29/2022]
Abstract
Lumichrome (LC) is the major photodegradation product of biologically important flavin cofactors. Since LC serves as a structural comparison to the flavins; understanding excited states of LC is fundamentally important to establish a connection with photophysics of different flavins, such as lumiflavin (LF), riboflavin (RF), flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). Herein, we deduce the initial excited state structural dynamics of LC using UV resonance Raman (UVRR) intensity analysis. The UVRR spectra at wavelengths across the 260 nm absorption band of LC were measured and resulting Raman excitation profiles and absorption spectrum were self consistently simulated using a time-dependent wave packet formalism to extract the initial excited state structural and solvent broadening parameters. These results are compared with those obtained for other flavins following UV excitations. We find that LC undergoes a very distinct instantaneous charge redistribution than flavins, which is attributed to the extended π-conjugation present in flavins but missing in LC. The homogeneous broadening linewidth of LC appears to be lower than that of LF, while the inhomogeneous broadening values are comparable, indicating greater solvent interaction with excited flavin on ultrafast timescale compared to LC, whereas on longer timescale these interactions are almost similar.
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Affiliation(s)
- Sudeb Ghosh
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune-411 008, India
| | - Mrinalini Puranik
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune-411 008, India
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4
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Thymine dissociation and dimer formation: A Raman and synchronous fluorescence spectroscopic study. Proc Natl Acad Sci U S A 2021; 118:2025263118. [PMID: 33526704 PMCID: PMC8017689 DOI: 10.1073/pnas.2025263118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
In this study, absorption, fluorescence, synchronous fluorescence, and Raman spectra of nonirradiated and ultraviolet (UV)-irradiated thymine solutions were recorded in order to detect thymine dimer formation. The thymine dimer formation, as a function of irradiation dose, was determined by Raman spectroscopy. In addition, the formation of a mutagenic (6-4) photoproduct was identified by its synchronous fluorescence spectrum. Our spectroscopic data suggest that the rate of conversion of thymine to thymine dimer decreases after 20 min of UV irradiation, owing to the formation of an equilibrium between the thymine dimers and monomers. However, the formation of the (6-4) photoproduct continued to increase with UV irradiation. In addition, the Raman spectra of nonirradiated and irradiated calf thymus DNA were recorded, and the formation of thymine dimers was detected. The spectroscopic data presented make it possible to determine the mechanism of thymine dimer formation, which is known to be responsible for the inhibition of DNA replication that causes bacteria inactivation.
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5
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Gindt YM, Connolly G, Vonder Haar AL, Kikhwa M, Schelvis JPM. Investigation of the pH-dependence of the oxidation of FAD in VcCRY-1, a member of the cryptochrome-DASH family. Photochem Photobiol Sci 2021; 20:831-841. [PMID: 34091863 DOI: 10.1007/s43630-021-00063-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/31/2021] [Indexed: 11/29/2022]
Abstract
Vibrio cholerae cryptochrome-1 (VcCRY-1) is a member of the cryptochrome DASH family. The flavoprotein appears to use blue light both for repair of cyclobutane pyrimidine dimers (CPDs) on DNA and signal transduction. Earlier, we found that it was almost impossible to oxidize the FADH· state upon binding to a CPD, and, in the absence of substrate, the rate of FADH· oxidation was much larger at high pH (Gindt et al. in Biochemistry 54:2802-2805, 2015). Here, we present the pH-dependence of the oxidation of FADH· by ferricyanide, which revealed a switch between slow and fast oxidation with a pKa ≈ 7.0. Stopped-flow mixing was used to measure the oxidation of FADH- to FADH· at pH 6.7 and 7.5. Substrate binding was required to slow down this oxidation such that it could be measured with stopped flow, but there was only a small effect of pH. In addition, resonance Raman measurements of FADH· in VcCRY-1 at pH 6.5 and 7.5 were performed to probe for structural changes near the FAD cofactor related to the observed changes in rate of FADH· oxidation. Only substrate binding seemed to induce a change near the FAD cofactor that may relate to the change in oxidation kinetics. The pH-effect on the FADH· oxidation rate, which is rate-limited by the proton acceptor, does not seem to be due to a protein structural change near the FAD cofactor. Instead, a conserved glutamate in CRY-DASH may control the deprotonation of FADH· and give rise to the pH-effect.
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Affiliation(s)
- Yvonne M Gindt
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Gabrielle Connolly
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Amy L Vonder Haar
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Miryam Kikhwa
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Johannes P M Schelvis
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, 07043, USA.
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6
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How does the skin sense sun light? An integrative view of light sensing molecules. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2021. [DOI: 10.1016/j.jphotochemrev.2021.100403] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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7
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Keirsse-Haquin J, Picaud T, Bordes L, de Gracia AG, Desbois A. Modulation of the flavin-protein interactions in NADH peroxidase and mercuric ion reductase: a resonance Raman study. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2017; 47:205-223. [PMID: 28889232 DOI: 10.1007/s00249-017-1245-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/12/2017] [Accepted: 07/26/2017] [Indexed: 10/18/2022]
Abstract
NADH peroxidase (Npx) and mercuric ion reductase (MerA) are flavoproteins belonging to the pyridine nucleotide:disulfide oxidoreductases (PNDO) and catalyzing the reduction of toxic substrates, i.e., hydrogen peroxide and mercuric ion, respectively. To determine the role of the flavin adenine dinucleotide (FAD) in the detoxification mechanism, the resonance Raman (RR) spectra of these enzymes under various redox and ligation states have been investigated using blue and/or near-UV excitation(s). These data were compared to those previously obtained for glutathione reductase (GR), another enzyme of the PNDO family, but catalyzing the reduction of oxidized glutathione. Spectral differences have been detected for the marker bands of the isoalloxazine ring of Npx, MerA, and GR. They provide evidence for different catalytic mechanisms in these flavoproteins. The RR modes of the oxidized and two-electron reduced (EH2) forms of Npx are related to very tight flavin-protein interactions maintaining a nearly planar conformation of the isoalloxazine tricycle, a low level of H-bonding at the N1/N5 and O2/O4 sites, and a strong H-bond at N3H. They also indicate minimal changes in FAD structure and environment upon either NAD(H) binding or reduction of the sulfinic redox center. All these spectroscopic data support an enzyme functioning centered on the Cys-SO-/Cys-S- redox moiety and a neighbouring His residue. On the contrary, the RR data on various functional forms of MerA are indicative of a modulation of both ring II distortion and H-bonding states of the N5 site and ring III. The Cd(II) binding to the EH2-NADP(H) complexes, biomimetic intermediates in the reaction of Hg(II) reduction, provokes important spectral changes. They are interpreted in terms of flattening of the isoalloxazine ring and large decreases in H-bonding at the N5 site and ring III. The large flexibility of the FAD structure and environment in MerA is in agreement with proposed mechanisms involving C4a(flavin) adducts.
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Affiliation(s)
- Julie Keirsse-Haquin
- Institut de Biologie Intégrative de la Cellule, UMR 9198 CNRS-CEA-Université Paris Sud, CEA Saclay, 91191, Gif-sur-Yvette Cedex, France.,Ecole Nationale Supérieure des Mines, 44300, Nantes, France
| | - Thierry Picaud
- Institut de Biologie Intégrative de la Cellule, UMR 9198 CNRS-CEA-Université Paris Sud, CEA Saclay, 91191, Gif-sur-Yvette Cedex, France.,Institut Supérieur des Biotechnologies de Paris (Sup'Biotech Paris), 94800, Villejuif, France
| | - Luc Bordes
- Institut de Biologie Intégrative de la Cellule, UMR 9198 CNRS-CEA-Université Paris Sud, CEA Saclay, 91191, Gif-sur-Yvette Cedex, France.,School of Earth and Environmental Sciences, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Adrienne Gomez de Gracia
- Institut de Biologie Intégrative de la Cellule, UMR 9198 CNRS-CEA-Université Paris Sud, CEA Saclay, 91191, Gif-sur-Yvette Cedex, France
| | - Alain Desbois
- Institut de Biologie Intégrative de la Cellule, UMR 9198 CNRS-CEA-Université Paris Sud, CEA Saclay, 91191, Gif-sur-Yvette Cedex, France.
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8
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Xu L, Wen B, Wang Y, Tian C, Wu M, Zhu G. Residues at a Single Site Differentiate Animal Cryptochromes from Cyclobutane Pyrimidine Dimer Photolyases by Affecting the Proteins' Preferences for Reduced FAD. Chembiochem 2017; 18:1129-1137. [PMID: 28393477 DOI: 10.1002/cbic.201700145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Indexed: 12/29/2022]
Abstract
Cryptochromes (CRYs) and photolyases belong to the cryptochrome/photolyase family (CPF). Reduced FAD is essential for photolyases to photorepair UV-induced cyclobutane pyrimidine dimers (CPDs) or 6-4 photoproducts in DNA. In Drosophila CRY (dCRY, a type I animal CRY), FAD is converted to the anionic radical but not to the reduced state upon illumination, which might induce a conformational change in the protein to relay the light signal downstream. To explore the foundation of these differences, multiple sequence alignment of 650 CPF protein sequences was performed. We identified a site facing FAD (Ala377 in Escherichia coli CPD photolyase and Val415 in dCRY), hereafter referred to as "site 377", that was distinctly conserved across these sequences: CPD photolyases often had Ala, Ser, or Asn at this site, whereas animal CRYs had Ile, Leu, or Val. The binding affinity for reduced FAD, but not the photorepair activity of E. coli photolyase, was dramatically impaired when replacing Ala377 with any of the three CRY residues. Conversely, in V415S and V415N mutants of dCRY, FAD was photoreduced to its fully reduced state after prolonged illumination, and light-dependent conformational changes of these mutants were severely inhibited. We speculate that the residues at site 377 play a key role in the different preferences of CPF proteins for reduced FAD, which differentiate animal CRYs from CPD photolyases.
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Affiliation(s)
- Lei Xu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China.,Anhui Province Key Laboratory of Active Biological Macro-Molecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, China
| | - Bin Wen
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China.,Anhui Province Key Laboratory of Active Biological Macro-Molecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, China
| | - Yuan Wang
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China
| | - Changqing Tian
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China
| | - Mingcai Wu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China.,Anhui Province Key Laboratory of Active Biological Macro-Molecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, China
| | - Guoping Zhu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China
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9
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Zhang M, Wang L, Shu S, Sancar A, Zhong D. Bifurcating electron-transfer pathways in DNA photolyases determine the repair quantum yield. Science 2017; 354:209-213. [PMID: 27738168 DOI: 10.1126/science.aah6071] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/15/2016] [Indexed: 11/02/2022]
Abstract
Photolyase is a blue-light-activated enzyme that repairs ultraviolet-induced DNA damage that occurs in the form of cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts. Previous studies on microbial photolyases have revealed an electron-tunneling pathway that is critical for the repair mechanism. In this study, we used femtosecond spectroscopy to deconvolute seven electron-transfer reactions in 10 elementary steps in all classes of CPD photolyases. We report a unified electron-transfer pathway through a conserved structural configuration that bifurcates to favor direct tunneling in prokaryotes and a two-step hopping mechanism in eukaryotes. Both bifurcation routes are operative, but their relative contributions, dictated by the reduction potentials of the flavin cofactor and the substrate, determine the overall quantum yield of repair.
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Affiliation(s)
- Meng Zhang
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Lijuan Wang
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Shi Shu
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
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10
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Schelvis JPM, Gindt YM. A Review of Spectroscopic and Biophysical-Chemical Studies of the Complex of Cyclobutane Pyrimidine Dimer Photolyase and Cryptochrome DASH with Substrate DNA. Photochem Photobiol 2017; 93:26-36. [PMID: 27891613 DOI: 10.1111/php.12678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 11/02/2016] [Indexed: 01/02/2023]
Abstract
Cyclobutane pyrimidine dimer (CPD) photolyase (PL) is a structure-specific DNA repair enzyme that uses blue light to repair CPD on DNA. Cryptochrome (CRY) DASH enzymes use blue light for the repair of CPD lesions on single-stranded (ss) DNA, although some may also repair these lesions on double-stranded (ds) DNA. In addition, CRY DASH may be involved in blue light signaling, similar to cryptochromes. The focus of this review is on spectroscopic and biophysical-chemical experiments of the enzyme-substrate complex that have contributed to a more detailed understanding of all the aspects of the CPD repair mechanism of CPD photolyase and CRY DASH. This will be performed in the backdrop of the available X-ray crystal structures of these enzymes bound to a CPD-like lesion. These structures helped to confirm conclusions that were drawn earlier from spectroscopic and biophysical-chemical experiments, and they have a critical function as a framework to design new experiments and to interpret new experimental data. This review will show the important synergy between X-ray crystallography and spectroscopic/biophysical-chemical investigations that is essential to obtain a sufficiently detailed picture of the overall mechanism of CPD photolyases and CRY DASH proteins.
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Affiliation(s)
| | - Yvonne M Gindt
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ
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11
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Abstract
Plants use light for photosynthesis and for various signaling purposes. The UV wavelengths in sunlight also introduce DNA damage in the form of cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts [(6-4)PPs] that must be repaired for the survival of the plant. Genome sequencing has revealed the presence of genes for both CPD and (6-4)PP photolyases, as well as genes for nucleotide excision repair in plants, such as Arabidopsis and rice. Plant photolyases have been purified, characterized, and have been shown to play an important role in plant survival. In contrast, even though nucleotide excision repair gene homologs have been found in plants, the mechanism of nucleotide excision repair has not been investigated. Here we used the in vivo excision repair assay developed in our laboratory to demonstrate that Arabidopsis removes CPDs and (6-4)PPs by a dual-incision mechanism that is essentially identical to the mechanism of dual incisions in humans and other eukaryotes, in which oligonucleotides with a mean length of 26-27 nucleotides are removed by incising ∼20 phosphodiester bonds 5' and 5 phosphodiester bonds 3' to the photoproduct.
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12
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Menezes AC, Raposo S, Simões S, Ribeiro H, Oliveira H, Ascenso A. Prevention of Photocarcinogenesis by Agonists of 5-HT1A and Antagonists of 5-HT2A Receptors. Mol Neurobiol 2015; 53:1145-1164. [DOI: 10.1007/s12035-014-9068-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/29/2014] [Indexed: 12/13/2022]
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13
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Wijaya IMM, Iwata T, Yamamoto J, Hitomi K, Iwai S, Getzoff ED, Kennis JTM, Mathes T, Kandori H. Flavin adenine dinucleotide chromophore charge controls the conformation of cyclobutane pyrimidine dimer photolyase α-helices. Biochemistry 2014; 53:5864-75. [PMID: 25152314 DOI: 10.1021/bi500638b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Observations of light-receptive enzyme complexes are usually complicated by simultaneous overlapping signals from the chromophore, apoprotein, and substrate, so that only the initial, ultrafast, photon-chromophore reaction and the final, slow, protein conformational change provide separate, nonoverlapping signals. Each provides its own advantages, whereas sometimes the overlapping signals from the intervening time scales still cannot be fully deconvoluted. We overcome the problem by using a novel method to selectively isotope-label the apoprotein but not the flavin adenine dinucleotide (FAD) cofactor. This allowed the Fourier transform infrared (FTIR) signals to be separated from the apoprotein, FAD cofactor, and DNA substrate. Consequently, a comprehensive structure-function study by FTIR spectroscopy of the Escherichia coli cyclobutane pyrimidine dimer photolyase (CPD-PHR) DNA repair enzyme was possible. FTIR signals could be identified and assigned upon FAD photoactivation and DNA repair, which revealed protein dynamics for both processes beyond simple one-electron reduction and ejection, respectively. The FTIR data suggest that the synergistic cofactor-protein partnership in CPD-PHR linked to changes in the shape of FAD upon one-electron reduction may be coordinated with conformational changes in the apoprotein, allowing it to fit the DNA substrate. Activation of the CPD-PHR chromophore primes the apoprotein for subsequent DNA repair, suggesting that CPD-PHR is not simply an electron-ejecting structure. When FAD is activated, changes in its structure may trigger coordinated conformational changes in the apoprotein and thymine carbonyl of the substrate, highlighting the role of Glu275. In contrast, during DNA repair and release processes, primary conformational changes occur in the enzyme and DNA substrate, with little contribution from the FAD cofactor and surrounding amino acid residues.
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Affiliation(s)
- I M Mahaputra Wijaya
- Department of Frontier Materials and ‡OptoBio Technology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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14
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Barbatti M. Computational reference data for the photochemistry of cyclobutane pyrimidine dimers. Chemphyschem 2014; 15:3342-54. [PMID: 25044616 DOI: 10.1002/cphc.201402302] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Indexed: 01/19/2023]
Abstract
The cis-syn cyclobutane pyrimidine dimer is one of the major classes of carcinogenic UV-induced DNA photoproducts. In this work, diverse high-level quantum-chemical methods were used to determine the spectroscopic properties of neutral (singlet and triplet) and charged (cation and anion) species of thymine dimers. Maps of potential energy, charge distribution, electron affinity, and ionization potential of the thymidine dimers were computed along the two dimerization coordinates for neutral and charged species, as well as for the singlet excited state. This set of data aims at providing consistent results computed with the same methods as for photodamage and repair. Based on these results, several different photo-, heat-, and charge-induced mechanisms of dimerization and repair are characterized and discussed. Additionally, a new stable dimer with methylmethylidene-hexahydropyrimidine structure was found in the S0 state.
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Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany).
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15
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Li J, Kitagawa T. Resonance Raman spectroscopy. Methods Mol Biol 2014; 1146:377-400. [PMID: 24764099 DOI: 10.1007/978-1-4939-0452-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Flavin is a general name given to molecules having the heteroaromatic ring system of 7,8-dimethylisoalloxazine but practically means riboflavin (Rfl), flavin adenine dinucleotide (FAD), and flavin mononucleotide (FMN) in biological systems, whose structures are illustrated in Fig. 1, together with the atomic numbering scheme and ring numbering of the isoalloxazine moiety. As the isoalloxazine skeleton cannot be synthesized in human cells, it is obtained from diet as Rfl (vitamin B2). FAD and FMN can act as cofactors in flavoenzymes but Rfl does not. Most flavoenzymes catalyze redox reactions of substrates (Miura, Chem Rec 1:183-194, 2001). When O2 serves as the oxidant in the oxidation half cycle of an enzymic reaction, the enzyme is called "flavo-oxidase" but when others do, the enzyme is called "flavo-dehydrogenase." The difference between the two types of oxidative catalysis arises from delicate differences in the π-electron distributions in the isoalloxazine ring, which can be revealed by Raman spectroscopy (Miura, Chem Rec 1:183-194, 2001). Since a flavin is an extremely versatile molecule, the scientific field including chemistry, biochemistry, and enzymology is collectively called "flavonology." It was found recently, however, that the flavin also acts as a chromophore to initiate light-induced DNA repair and signal transductions (Sancar, Chem Rev 103:2203-2237, 2003).
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Affiliation(s)
- Jiang Li
- Graduate School of Life Science, University of Hyogo, Kamigori-cho, Aku-gum, 678-1297, Hyogo, Japan
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16
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Abstract
Photoinduced processes in nucleic acids are phenomena of fundamental interest in diverse fields, from prebiotic studies, through medical research on carcinogenesis, to the development of bioorganic photodevices. In this contribution we survey many aspects of the research across the boundaries. Starting from a historical background, where the main milestones are identified, we review the main findings of the physical-chemical research of photoinduced processes on several types of nucleic-acid fragments, from monomers to duplexes. We also discuss a number of different issues which are still under debate.
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Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany,
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17
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Dynamic determination of the functional state in photolyase and the implication for cryptochrome. Proc Natl Acad Sci U S A 2013; 110:12972-7. [PMID: 23882072 DOI: 10.1073/pnas.1311077110] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The flavin adenine dinucleotide cofactor has an unusual bent configuration in photolyase and cryptochrome, and such a folded structure may have a functional role in initial photochemistry. Using femtosecond spectroscopy, we report here our systematic characterization of cyclic intramolecular electron transfer (ET) dynamics between the flavin and adenine moieties of flavin adenine dinucleotide in four redox forms of the oxidized, neutral, and anionic semiquinone, and anionic hydroquinone states. By comparing wild-type and mutant enzymes, we have determined that the excited neutral oxidized and semiquinone states absorb an electron from the adenine moiety in 19 and 135 ps, whereas the excited anionic semiquinone and hydroquinone states donate an electron to the adenine moiety in 12 ps and 2 ns, respectively. All back ET dynamics occur ultrafast within 100 ps. These four ET dynamics dictate that only the anionic hydroquinone flavin can be the functional state in photolyase due to the slower ET dynamics (2 ns) with the adenine moiety and a faster ET dynamics (250 ps) with the substrate, whereas the intervening adenine moiety mediates electron tunneling for repair of damaged DNA. Assuming ET as the universal mechanism for photolyase and cryptochrome, these results imply anionic flavin as the more attractive form of the cofactor in the active state in cryptochrome to induce charge relocation to cause an electrostatic variation in the active site and then lead to a local conformation change to initiate signaling.
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18
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Liu Z, Guo Z, Zhong H, Qin X, Wan M, Yang B. Graphene oxide based surface-enhanced Raman scattering probes for cancer cell imaging. Phys Chem Chem Phys 2013; 15:2961-6. [DOI: 10.1039/c2cp43715e] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Fingerhut BP, Heil K, Kaya E, Oesterling S, de Vivie-Riedle R, Carell T. Mechanism of UV-induced Dewar lesion repair catalysed by DNA (6-4) photolyase. Chem Sci 2012. [DOI: 10.1039/c2sc20122d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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Sadeghian K, Bocola M, Merz T, Schütz M. Theoretical study on the repair mechanism of the (6-4) photolesion by the (6-4) photolyase. J Am Chem Soc 2010; 132:16285-95. [PMID: 20977236 DOI: 10.1021/ja108336t] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
UV irradiation of DNA can lead to the formation of mutagenic (6-4) pyrimidine-pyrimidone photolesions. The (6-4) photolyases are the enzymes responsible for the photoinduced repair of such lesions. On the basis of the recently published crystal structure of the (6-4) photolyase bound to DNA [Maul et al. 2008] and employing quantum mechanics/molecular mechanics techniques, a repair mechanism is proposed, which involves two photoexcitations. The flavin chromophore, initially being in its reduced anionic form, is photoexcited and donates an electron to the (6-4) form of the photolesion. The photolesion is then protonated by the neighboring histidine residue and forms a radical intermediate. The latter undergoes a series of energy stabilizing hydrogen-bonding rearrangements before the electron back transfer to the flavin semiquinone. The resulting structure corresponds to the oxetane intermediate, long thought to be formed upon DNA-enzyme binding. A second photoexcitation of the flavin promotes another electron transfer to the oxetane. Proton donation from the same histidine residue allows for the splitting of the four-membered ring, hence opening an efficient pathway to the final repaired form. The repair of the lesion by a single photoexcitation was shown not to be feasible.
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Affiliation(s)
- Keyarash Sadeghian
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstraβe 31, D-93040 Regensburg, Germany
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21
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Sokolowsky K, Newton M, Lucero C, Wertheim B, Freedman J, Cortazar F, Czochor J, Schelvis JPM, Gindt YM. Spectroscopic and thermodynamic comparisons of Escherichia coli DNA photolyase and Vibrio cholerae cryptochrome 1. J Phys Chem B 2010; 114:7121-30. [PMID: 20438097 DOI: 10.1021/jp102275r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Escherichia coli DNA photolyase and cryptochrome 1 isolated from Vibrio cholerae, a member of the CRY-DASH family, are directly compared using a variety of experimental methods including UV-vis and Raman spectroscopy, reduction potential measurements, and isothermal titration calorimetry. The semiquinone form of the cryptochrome has an absorption spectrum that is red-shifted from that of the photolyase, but the Raman spectrum indicates that the FAD binding pocket is similar to that of photolyase. The FADH(-)/FADH* reduction potential of the cryptochrome is significantly higher than that of the photolyase at 164 mV vs NHE, but it also increases upon substrate binding (to 195 mV vs NHE), an increase similar to what is observed in photolyase. The FADH(-)/FADH* reduction potential for both proteins was found to be insensitive to ATP binding. Isothermal titration calorimetry found that photolyase binds tighter to substrate (K(A) approximately 10(5) M(-1) for photolyase and approximately 10(4) M(-1) for cryptochrome 1), and the binding constants for both proteins were slightly sensitive to oxidation state. Based upon this work, it appears that this cryptochrome has significant spectroscopic and electrochemical similarities to CPD photolyase. The thermodynamic cycle of the enzymatic repair in the context of this work is discussed.
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Affiliation(s)
- Kathleen Sokolowsky
- Department of Chemistry, Hugel Science Center, Lafayette College, Easton, Pennsylvania 18042, USA
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22
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Ultrafast solvation dynamics at binding and active sites of photolyases. Proc Natl Acad Sci U S A 2010; 107:2914-9. [PMID: 20133751 DOI: 10.1073/pnas.1000001107] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dynamic solvation at binding and active sites is critical to protein recognition and enzyme catalysis. We report here the complete characterization of ultrafast solvation dynamics at the recognition site of photoantenna molecule and at the active site of cofactor/substrate in enzyme photolyase by examining femtosecond-resolved fluorescence dynamics and the entire emission spectra. With direct use of intrinsic antenna and cofactor chromophores, we observed the local environment relaxation on the time scales from a few picoseconds to nearly a nanosecond. Unlike conventional solvation where the Stokes shift is apparent, we observed obvious spectral shape changes with the minor, small, and large spectral shifts in three function sites. These emission profile changes directly reflect the modulation of chromophore's excited states by locally constrained protein and trapped-water collective motions. Such heterogeneous dynamics continuously tune local configurations to optimize photolyase's function through resonance energy transfer from the antenna to the cofactor for energy efficiency and then electron transfer between the cofactor and the substrate for repair of damaged DNA. Such unusual solvation and synergetic dynamics should be general in function sites of proteins.
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23
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Usman A, Brazard J, Martin MM, Plaza P, Heijde M, Zabulon G, Bowler C. Spectroscopic characterization of a (6-4) photolyase from the green alga Ostreococcus tauri. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2009; 96:38-48. [PMID: 19427226 DOI: 10.1016/j.jphotobiol.2009.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 03/10/2009] [Accepted: 04/06/2009] [Indexed: 10/20/2022]
Abstract
The cofactor content of OtCPF1, a (6-4) photolyase isolated from the green marine alga Ostreococcus tauri, was characterized by steady-state absorption and fluorescence spectroscopy. The heterologously expressed, GST-fused, purified protein (MW: 89kDa) is non-covalently bound to flavin adenine dinucleotide (FAD), with a flavin to apoprotein molecular ratio of 64%. No light-harvesting chromophore was found in this protein. In freshly purified OtCPF1, FAD is present in three different redox states: the fully oxidized form (FAD(ox), 82%), the neutral semiquinone (FADH*, 14%) and the fully reduced anion (FADH-, 4%). Keeping the sample in the dark, at 5 degrees C, yields oxidation of FADH* and FADH-, partial release of FAD to the solution and slow degradation of the protein. Upon steady-state blue-light irradiation of OtCPF1 at 450nm, photoreduction processes leading to an accumulation of stable FADH* and FADH- species are observed. We demonstrate that this accumulation is due to the presence of an external electron donor agent in the purification buffer. Composition changes observed under steady-state photoexcitation are interpreted in terms of photoinduced reductions of FAD(ox) and FADH* states and competitive back reactions. Specific irradiation by red light at 620 nm shows both photoreduction of FADH* to FADH- and irreversible oxidation of FADH* to FAD(ox). The photoinduced oxidation reaction is believed to be indirectly caused by the external donor agent present in the buffer. Photoexcitation is also shown to stabilize the binding of FAD to the protein. We suggest this effect to be due to slight changes in the protein conformation, possibly strengthening the hydrogen-bonding network surrounding FAD.
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Affiliation(s)
- Anwar Usman
- UMR 8640 CNRS-ENS-UPMC, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, Paris, France
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24
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Murphy AK, Tammaro M, Cortazar F, Gindt YM, Schelvis JPM. Effect of the cyclobutane cytidine dimer on the properties of Escherichia coli DNA photolyase. J Phys Chem B 2009; 112:15217-26. [PMID: 18973361 DOI: 10.1021/jp806526y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclobutane pyrimidine dimer (CPD) photolyases are structure specific DNA-repair enzymes that specialize in the repair of CPDs, the major photoproducts that are formed upon irradiation of DNA with ultraviolet light. The purified enzyme binds a flavin adenine dinucleotide (FAD), which is in the neutral radical semiquinone (FADH(*)) form. The CPDs are repaired by a light-driven, electron transfer from the anionic hydroquinone (FADH(-)) singlet excited state to the CPD, which is followed by reductive cleavage of the cyclobutane ring and subsequent monomerization of the pyrimidine bases. CPDs formed between two adjacent thymidine bases (T< >T) are repaired with greater efficiency than those formed between two adjacent cytidine bases (C< >C). In this paper, we investigate the changes in Escherichia coli photolyase that are induced upon binding to DNA containing C< >C lesions using resonance Raman, UV-vis absorption, and transient absorption spectroscopies, spectroelectrochemistry, and computational chemistry. The binding of photolyase to a C< >C lesion modifies the energy levels of FADH(*), the rate of charge recombination between FADH(-) and Trp(306)(*), and protein-FADH(*) interactions differently than binding to a T< >T lesion. However, the reduction potential of the FADH(-)/FADH(*) couple is modified in the same way with both substrates. Our calculations show that the permanent electric dipole moment of C< >C is stronger (12.1 D) and oriented differently than that of T< >T (8.7 D). The possible role of the electric dipole moment of the CPD in modifying the physicochemical properties of photolyase as well as in affecting CPD repair will be discussed.
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Affiliation(s)
- Anar K Murphy
- Department of Chemistry, New York University, New York, New York 10003, USA
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25
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Oztürk N, Song SH, Ozgür S, Selby CP, Morrison L, Partch C, Zhong D, Sancar A. Structure and function of animal cryptochromes. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2008; 72:119-31. [PMID: 18419269 DOI: 10.1101/sqb.2007.72.015] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cryptochrome (CRY) is a photolyase-like flavoprotein with no DNA-repair activity but with known or presumed blue-light receptor function. Animal CRYs have DNA-binding and autokinase activities, and their flavin cofactor is reduced by photoinduced electron transfer. In Drosophila, CRY is a major circadian photoreceptor, and in mammals, the two CRY proteins are core components of the molecular clock and potential circadian photoreceptors. In mammals, CRYs participate in cell cycle regulation and the cellular response to DNA damage by controlling the expression of some cell cycle genes and by directly interacting with checkpoint proteins.
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Affiliation(s)
- N Oztürk
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
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26
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Kao YT, Tan C, Song SH, Öztürk N, Li J, Wang L, Sancar A, Zhong D. Ultrafast dynamics and anionic active states of the flavin cofactor in cryptochrome and photolyase. J Am Chem Soc 2008; 130:7695-701. [PMID: 18500802 PMCID: PMC2661107 DOI: 10.1021/ja801152h] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report here our systematic studies of the dynamics of four redox states of the flavin cofactor in both photolyases and insect type 1 cryptochromes. With femtosecond resolution, we observed ultrafast photoreduction of oxidized state flavin adenine dinucleotide (FAD) in subpicosecond and of neutral radical semiquinone (FADH(*)) in tens of picoseconds through intraprotein electron transfer mainly with a neighboring conserved tryptophan triad. Such ultrafast dynamics make these forms of flavin unlikely to be the functional states of the photolyase/cryptochrome family. In contrast, we find that upon excitation the anionic semiquinone (FAD(*-)) and hydroquinone (FADH(-)) have longer lifetimes that are compatible with high-efficiency intermolecular electron transfer reactions. In photolyases, the excited active state (FADH(-)*) has a long (nanosecond) lifetime optimal for DNA-repair function. In insect type 1 cryptochromes known to be blue-light photoreceptors the excited active form (FAD(*-)*) has complex deactivation dynamics on the time scale from a few to hundreds of picoseconds, which is believed to occur through conical intersection(s) with a flexible bending motion to modulate the functional channel. These unique properties of anionic flavins suggest a universal mechanism of electron transfer for the initial functional steps of the photolyase/cryptochrome blue-light photoreceptor family.
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Affiliation(s)
- Ya-Ting Kao
- Departments of Physics, Chemistry, and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, 191 West Woodruff Avenue, Columbus, Ohio, 43210
| | - Chuang Tan
- Departments of Physics, Chemistry, and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, 191 West Woodruff Avenue, Columbus, Ohio, 43210
| | - Sang-Hun Song
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Mary Ellen Jones Building, CB 7260, Chapel Hill, NC 27599
| | - Nuri Öztürk
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Mary Ellen Jones Building, CB 7260, Chapel Hill, NC 27599
| | - Jiang Li
- Departments of Physics, Chemistry, and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, 191 West Woodruff Avenue, Columbus, Ohio, 43210
| | - Lijuan Wang
- Departments of Physics, Chemistry, and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, 191 West Woodruff Avenue, Columbus, Ohio, 43210
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Mary Ellen Jones Building, CB 7260, Chapel Hill, NC 27599
| | - Dongping Zhong
- Departments of Physics, Chemistry, and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, 191 West Woodruff Avenue, Columbus, Ohio, 43210
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27
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Eisenberg AS, Schelvis JPM. Contributions of the 8-methyl group to the vibrational normal modes of flavin mononucleotide and its 5-methyl semiquinone radical. J Phys Chem A 2008; 112:6179-89. [PMID: 18547041 DOI: 10.1021/jp711832g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Resonance Raman spectroscopy is a powerful tool to investigate flavins and flavoproteins, and a good understanding of the flavin vibrational normal modes is essential for the interpretation of the Raman spectra. Isotopic labeling is the most effective tool for the assignment of vibrational normal modes, but such studies have been limited to labeling of rings II and III of the flavin isoalloxazine ring. In this paper, we report the resonance and pre-resonance Raman spectra of flavin mononucleotide (FMN) and its N5-methyl neutral radical semiquinone (5-CH 3FMN(*)), of which the 8-methyl group of ring I has been deuterated. The experiments indicate that the Raman bands in the low-frequency region are the most sensitive to 8-methyl deuteration. Density functional theory (DFT) calculations have been performed on lumiflavin to predict the isotope shifts, which are used to assign the calculated normal modes to the Raman bands of FMN. A first assignment of the low-frequency Raman bands on the basis of isotope shifts is proposed. Partial deuteration of the 8-methyl group reveals that the changes in the Raman spectra do not always occur gradually. These observations are reproduced by the DFT calculations, which provide detailed insight into the underlying modifications of the normal modes that are responsible for the changes in the Raman spectra. Two types of isotopic shift patterns are observed: either the frequency of the normal mode but not its composition changes or the composition of the normal mode changes, which then appears at a new frequency. The DFT calculations also reveal that the effect of H/D-exchange in the 8-methyl group on the composition of the vibrational normal modes is affected by the position of the exchanged hydrogen, i.e., whether it is in or out of the isoalloxazine plane.
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Affiliation(s)
- Azaria S Eisenberg
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, USA
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28
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Yan Lv X, Rong Qiao D, Xiong Y, Xu H, You FF, Cao Y, He X, Cao Y. Photoreactivation of (6-4) photolyase in Dunaliella salina. FEMS Microbiol Lett 2008; 283:42-6. [PMID: 18399992 DOI: 10.1111/j.1574-6968.2008.01144.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Dunaliella salina is a unicellular green alga and possesses two types of photolyase: Class II cyclobutane pyrimidine dimers (CPD) photolyase and (6-4) photolyase. The gene of D. salina (6-4) photolyase is the first one found in unicellular organisms. CPD photolyases have been extensively studied but (6-4) photolyases are less understood. Because of the data observed in this study, D. salina (6-4) photolyase is insensitive to high salinity; whether it can tolerate a higher level of salinity than other (6-4) photolyases needs to be studied further. However, evidence is provided that (6-4) photolyases might be highly conserved among different species, not only in the sequence identity but also in the photorepair mechanism.
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Affiliation(s)
- Xue Yan Lv
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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29
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Discrimination of class I cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue. Biophys J 2007; 94:2194-203. [PMID: 18055535 DOI: 10.1529/biophysj.107.119248] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA photolyase recognizes ultraviolet-damaged DNA and breaks improperly formed covalent bonds within the cyclobutane pyrimidine dimer by a light-activated electron transfer reaction between the flavin adenine dinucleotide, the electron donor, and cyclobutane pyrimidine dimer, the electron acceptor. Theoretical analysis of the electron-tunneling pathways of the DNA photolyase derived from Anacystis nidulans can reveal the active role of the protein environment in the electron transfer reaction. Here, we report the unexpectedly important role of the single methionine residue, Met-353, where busy trafficking of electron-tunneling currents is observed. The amino acid conservation pattern of Met-353 in the homologous sequences perfectly correlates with experimentally verified annotation as photolyases. The bioinformatics sequence analysis also suggests that the residue plays a pivotal role in biological function. Consistent findings from different disciplines of computational biology strongly suggest the pivotal role of Met-353 in the biological function of DNA photolyase.
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Ruelas DS, Karentz D, Sullivan JT. Lethal and sub-lethal effects of UVB on juvenile Biomphalaria glabrata (Mollusca: Pulmonata). J Invertebr Pathol 2006; 93:192-200. [PMID: 16996081 PMCID: PMC1824712 DOI: 10.1016/j.jip.2006.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2006] [Revised: 07/20/2006] [Accepted: 08/02/2006] [Indexed: 11/16/2022]
Abstract
Although Schistosoma mansoni occurs mainly in the tropics, where intense levels of solar radiation are present, the impact of ultraviolet (UV) light on schistosome transmission is not known. The purpose of this study was to investigate potential effects of UVB (290-320nm) on juvenile Biomphalaria glabrata, the snail intermediate host of S. mansoni. Albino and wild-type snails were exposed to doses of UVB from UV-fluorescent lamps, and the following were measured: survival, photoreactivation (light-mediated DNA repair), effects on feeding behavior, and morphological tissue abnormalities. Irradiation with UVB is lethal to B. glabrata in a dose-dependent manner. Exposure to white light subsequent to UVB irradiation enhances survival, probably by photoreactivation. The shell offers some, but not complete, protection. Experiments in which UVB transmittance through the shell was blocked with black nail polish suggest that injury to both exposed (headfoot) and shell-enclosed (mantle and visceral mass) tissues contributes to mortality in lethally irradiated snails. Wild-type (pigmented) snails are less susceptible to lethal effects of UVB than albino snails, and they may be more capable of photoreactivation. UVB exposure inhibits snail feeding behavior, and causes tentacle forks and growths on the headfoot. Thus, UVB may influence the life cycle of S. mansoni by both lethal and sub-lethal damage to the snail intermediate host. However, the ability of snails to photoreactivate may mitigate these effects.
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Affiliation(s)
- Debbie S Ruelas
- Department of Biology, University of San Francisco, 2130 Fulton Street, San Francisco, CA 94117, USA
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